2. Threonine beta-epimerase is a pyridoxyl phosphate-dependent enzyme that catalyzes the reactionbelow. Provide a mechanism for the PLP-enzyme catalyzed reaction; you need to show themechanism for the formation of the aldimine and the mechanism for the hydrolysis step thatregenerates PLP.-20 PO.OHCO₂NH3*Threoninebeta-epimerasePLPOHNH3H*NOHPyridoxyl phosphate (PLP)

Enzymes are proteins that catalyze biochemical reactions. Sometimes proteins require a non-protein…

Answered: 2. Threonine beta-epimerase is a…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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2. In contrast to the toxicity of 2-fluoro-citrate, L-(2-fluoro-)succinate is not an inhibitor of succinate dehydrogenase and the product 2-fluoro-fumarate is converted by fumarate hydratase to L-(2-fluoro-2- hydroxy)malate that breaks down to oxaloacetate. (a) the FAD coenzyme of succinate dehydrogenase as the normal substrate? Write the reaction with structural formulas to illustrate your answer. Does the oxidation of 2-fluoro-succinate yield the same number of reducing equivalents to (b) droxy)malate, which breaks down spontaneously to oxaloacetate. Write the equation with structural formulas. 2-fluoro-fumarate is a substrate of fumarate hydratase forming only L-(2-fluoro-2-hy- Oxaloacetate has been shown to be a very po- (c) tent inhibitor of succinate dehydrogenase. For the enzyme 3 isolated from cardiac muscle the Kj value is ~4 x 10-6M, as shown in the L-B plot on the right. Yet, this inhibition is never discussed in biochemistry textbooks. From your reading in the textbook,…
24. Consider the figure below, which is an alternate way to depict the energy changes occurring during a reaction from Substrate (S) to Product (P), when uncatalyzed (curve A) and when catalyzed by an enzyme (curve B). Note that curve B is not the same way we modeled an enzyme-catalyzed reaction in class; this model is a different, perhaps slightly more realistic, way of conceptualizing the energy changes over the course of a reaction than what we did in class. S and ES represent the transition states for reaction of the free substrate (S) or the enzyme-substrate complex (ES). T T activation energy for uncatalyzed reaction EST S edhosob nohtum od bluo woH abiow yedio 2 wwolaixa-y odi no vaigin oroda dapng odt ni o nfog) r gibadhoa P B ES EP progress of reaction activation energy for catalyzed reaction a) Explain briefly why, in curve B, the energy state of the enzyme-substrate complex is less than the energy state of the substrate alone. b) Suppose the enzyme in the diagram was mutated…
6
38. The shown reaction is one of the four repeating steps during fatty acid biosynthesis. Which of the following statements is correct? A B CH₂-2-CH₂-2-5-ACP A. The small molecule in box A is NADPH + H* B. It is the second reduction reaction during fatty acid biosynthesis C. Both A and B D. Neither A nor B Он CH3-C-CH₂-C-5-ACP
6. Examine the plot of the enzyme-catalyzed reaction below: Wheat-germ acid phosphatase shows Michaelis-Menten kinetics when acting on para-nitrophenol phosphate 16 14 12 10 8 4 2 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 (S] / mM a) Is this reaction better characterized by Michaelis-Menten kinetics or simple mass action? b) What is the approximate value of Vmax? Km? c) Assuming that this plot was made at 100 nM enzyme, draw the curve, including axis labels, for 300 nM enzyme. d) Imagine that this enzyme is inhibited by a competitive inhibitor with Ki (for inhibitor) = Km (for substrate). Note that v = (kcat [E] tot [S]/Km) / (1 + [S]/Km + [I]/Ki). Draw the curve of reaction velocity (v) versus [S] for [I] = 1 mM. e) Now consider an experiment where you simultaneously introduce substrate and competitive inhibitor at equal concentrations. Make a plot of v versus concentration of [S] = [I], i.e. the X-axis should be the concentration of both I and S, which are equal. v/ uM min-
2. (Part A) Coenzyme-dependent enzymes can catalyze the general transformations shown below. What would be the best coenzymes to use for the two steps in the scheme, and why? R CO₂H A R SCOA B R R
1. - - Substrate Enzyme - 1 2 3 BOO - Look at the above diagram and understand what is being shown. Explain AND draw a graph depicting how the rate of the reaction depicted here is changing. ☐ L 2. How will the rate of the reaction change with time after 3? How can we increase the rate of the reaction after 3? I 100 B L
Q3
I only need a
3. Acetylcholinesterase is a serine hydrolase enzyme im- portant in nerve signal transmission, hydrolyzing acetylcho- line, an ester molecule with a positively charged quaternary nitrogen group. The structure of the physiologically relevant substrate of this enzyme is shown on the right. The quater- H₂C nary nitrogen group serves to anchor the molecule in the active site Gly121 Oxy- anion hole Gly122 Ala204 Substrate ACh His447 Catalytic triad Ser203 Glu202 Glu334 Ser229 CH3 N+ CH3 CH3 The a Scale document down rine protease family, consisting of a catalytic triad Ser203- His447-Glu334 with Ser203 supplying the nucleophilic hydroxyl group and an oxyanion hole com- prised of peptide NH groups of Gly121, Gly122, and Ala204, illustrated in the diagram above, for which carbon (green), nitrogen (blue), and oxygen (red) atoms are shown while hydrogen atoms are white. The enzyme catalyzed reaction can be represented by the following scheme: (a)( k1 K2 E + S = ES K-1 K3 EYE + P where ES…
5. Suppose an enzyme needed a cysteine thiol (sulfhydryl) group for its catalytic activity, and catalysis required the Cys thiol to act as a nucleophile at the beginning of the catalytic cycle. That would mean the Cys residue had to be in its UNPROTONATED (conjugate base) form. If that particular Cys residue in that protein had a pKą of 7.5, what fraction (percent, or proportion) of the total enzyme molecules would have the Cys R group in its ACTIVE form at pH 7.0?
Which of these metabolic by-products can increase RER above 1.0? Ca2+ lactate H+ Pi

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